Engineering of a chimeric RB69 DNA polymerase sensitive to drugs targeting the cytomegalovirus enzyme

J Biol Chem. 2009 Sep 25;284(39):26439-46. doi: 10.1074/jbc.M109.012500. Epub 2009 Jul 21.


Detailed structural and biochemical studies with the human cytomegalovirus (HCMV UL54) DNA polymerase are hampered by difficulties to obtain this enzyme in large quantities. The crystal structure of the related RB69 DNA polymerase (gp43) is often used as a model system to explain mechanisms of inhibition of DNA synthesis and drug resistance. However, here we demonstrate that gp43 is approximately 400-fold less sensitive to the pyrophosphate analog foscarnet, when compared with UL54. The RB69 enzyme is also able to discriminate against the nucleotide analog inhibitor acyclovir. In contrast, the HCMV polymerase is able to incorporate this compound with similar efficiency as observed with its natural counterpart. In an attempt to identify major determinants for drug activity, we replaced critical regions of the nucleotide-binding site of gp43 with equivalent regions of the HCMV enzyme. We show that chimeric gp43-UL54 enzymes that contain residues of helix N and helix P of UL54 are resensitized against foscarnet and acyclovir. Changing a region of three amino acids of helix N showed the strongest effects, and changes of two segments of three amino acids in helix P further contributed to the reversal of the phenotype. The engineered chimeric enzyme can be produced in large quantities and may therefore be a valuable surrogate system in drug development efforts. This system may likewise be used for detailed structural and biochemical studies on mechanisms associated with drug action and resistance.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Acyclovir / pharmacology
  • Antiviral Agents / pharmacology
  • Binding Sites
  • Catalysis / drug effects
  • Cytomegalovirus / drug effects
  • Cytomegalovirus / enzymology*
  • Cytomegalovirus / genetics
  • DNA-Directed DNA Polymerase / chemistry
  • DNA-Directed DNA Polymerase / genetics
  • DNA-Directed DNA Polymerase / metabolism*
  • Deoxycytosine Nucleotides / metabolism
  • Drug Resistance, Viral
  • Foscarnet / pharmacology
  • Kinetics
  • Models, Molecular
  • Molecular Structure
  • Protein Engineering
  • Protein Structure, Tertiary
  • Recombinant Fusion Proteins / chemistry
  • Recombinant Fusion Proteins / genetics
  • Recombinant Fusion Proteins / metabolism*
  • Viral Proteins / chemistry
  • Viral Proteins / genetics
  • Viral Proteins / metabolism*


  • Antiviral Agents
  • Deoxycytosine Nucleotides
  • Recombinant Fusion Proteins
  • UL54 protein, Human herpesvirus 5
  • Viral Proteins
  • 2'-deoxycytidine 5'-triphosphate
  • Foscarnet
  • DNA-Directed DNA Polymerase
  • Acyclovir